biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicscharles girardotIllumina MiSeqNextSeq 2000RNA-seq of coding RNAMus musculusMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17191To test if H3K27Ac contributes to chromatin accessibility at enhancers, we globally reduced H3K27Ac levels by chemical inhibition of the histone acetylase p300 (with the small molecule A-485, final concentration 3 μM). This dataset includes bait capture single molecule footprinting (SMF) data, comparing DMSO and A-485 treated samples in mouse cells (i.e., XY 159 knock-out of the three DNA methyl transferases (DNMT TKO) mESCs). Three biological replicates were generated for each treatment condition. In summary, after 24 hours of treatment, cells were collected for SMF, which marks accessible cytosines via recombinant methyltransferases, followed by bisulfite sequencing to infer protein-DNA interactions and chromatin accessibility at single-molecule resolution. Libraries were prepared using the Agilent SureSelect Mouse Methyl-Seq kit, which enriches for cis-regulatory elements, and sequenced on an Illumina NextSeq platform (150 bp paired-end, high-output mode). Reads were pre-processed with TrimGalore, aligned using QuasR, and deduplicated with Picard’s MarkDuplicates tool. Further analyses were conducted using custom scripts available at https://github.com/Krebslabrep/TF-chromatin.git.biostudies-arrayexpressSample Treatment - p300 inhibition was performed by adding 3 μM A-485 (Selleck Chemicals, S8740) to the ES medium for 24 hours.Sequencing - paired-end sequencing on illumina NextSeq 2000 run mode 155-8-155Library Construction - The library preparations, for the genome-wide data, were performed according to the SureSelect XT Mouse Methyl-Seq Kit Enrichment System for Illumina Multiplexed Sequencing Library protocol (Agilent Technologies, Santa Clara CA, Version E0, April 2018). A total of 3 microg of footprinted DNA was used as input for bait capture, according to the company's specifications. (# 5190-4836). DNA was first sonicated using a Covaris S220 sonicator to obtain products of 200-300 bp. DNA was then end-repaired, A-tailed and ligated with methylated adapters to create a pre-capture DNA library. Adapter-ligated libraries were purified using (0.65X) AMPure XP beads then quality and quantity of libraries were determined by bioanalyzer using DNA high sensitivity chip (Agilent). Next, 350 nanog of each library was hybridized with the SureSelect Mouse methyl-seq capture library at 65 C for 16 hours. Hybridized products were purified by capture with Dynabeads MyOne Streptavidin T1 magnetic beads and then subjected to bisulfite conversion using EZ DNA Methylation- Gold Kit kit according to manufacturer's protocol. As described in manufacturer's protocol (Agilent SureSelectXT Mouse Methyl-Seq Kit), bisulfite converted libraries were PCR-amplifed for 8 cycles with supplied universal primers and purified using AMPure XP beads. Captured libraries were indexed by PCR for another 6 cycles, using supplied indexes to generate a multiplexed library. High quality libraries were identified with an Agilent bioanalyzer using DNA high sensitivity chip and then pooled for sequencing. Supplied primers and recommended amplification parameters of the manufacturer were used throughout library preparation.Sequencing - paired-end sequencing on Illumina MiSeq with run mode 155-8-155Sample Collection - Mouse ES cells were cultured on 0.2% gelatin-coated plates in ES medium (DMEM, supplemented with 15% FBS, LIF, 2-Mercaptoethanol, 2 mM L-Glutamine and 1x non-essential amino acids) at 37C and 5% CO2. Medium was changed daily and cells were split every second day.Nucleic Acid Extraction - Genome-wide data was obtained using Agilent SureSelectXT Mouse Methyl-Seq Kit.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesValentina Badernacharles girardotArnaud KrebsRozemarijn KleinendorstfalseBait-capture based single molecule footprinting in 159 DNMT TKO mESCs upon p300 inhibitionTo test if H3K27Ac contributes to chromatin accessibility at enhancers, we globally reduced H3K27Ac levels by chemical inhibition of the histone acetylase p300 (with the small molecule A-485, final concentration 3 μM). This dataset includes bait capture single molecule footprinting (SMF) data, comparing DMSO and A-485 treated samples in mouse cells (i.e., XY 159 knock-out of the three DNA methyl transferases (DNMT TKO) mESCs). Three biological replicates were generated for each treatment condition. In summary, after 24 hours of treatment, cells were collected for SMF, which marks accessible cytosines via recombinant methyltransferases, followed by bisulfite sequencing to infer protein-DNA interactions and chromatin accessibility at single-molecule resolution. Libraries were prepared using the Agilent SureSelect Mouse Methyl-Seq kit, which enriches for cis-regulatory elements, and sequenced on an Illumina NextSeq platform (150 bp paired-end, high-output mode). Reads were pre-processed with TrimGalore, aligned using QuasR, and deduplicated with Picard’s MarkDuplicates tool. Further analyses were conducted using custom scripts available at https://github.com/Krebslabrep/TF-chromatin.git.2026-07-29T00:00:00Z2026-07-29T01:00:51.281Z2026-06-19T14:29:12.554ZE-MTAB-17191ERP195370EFO_0002944EFO_0004170EFO_0005518EFO_0004184EFO_0003969